Fix installation conflict and add RDKit-pypi as a versioned requirement

[djm-healx]

This PR fixes some circular import that is encountered during setup/installation, where the version of the structure pipeline is imported from module code. Now it is hard-coded into setup.py together with a pinned version of rdkit.

This was encountered in Python 3.9.8 when running:

pip install -e .
>>...
>>ModuleNotFoundError: No module named 'rdkit'

This was due to the setup script imported the version of this pipeline from chembl_structure_pipeline/__init__.py, which subsequently required the import of rdkit for the other code in __init__.py.

Also added rdkit-pypi as an optional extra dependency in setup.py, since I see in the CI script for this repo that conda is used . This should make the PR less likely to cause issues, and enables pip to handle versioning, if installed as pip install -e ".[rdkit]"

The version of rdkit-pypi is pinned to lie between 2019.03.1 (as specified in the module code) and 2021.3.5.1 (which is the last non-failing version where the tests in #39 still pass - see not below).

[djm-healx]

These changes seem to make Python 3.9.8 happy with installation and being able to run tests.

However, unittest fails on one of the tests, which feels separate to this PR:

python -m unittest discover chembl_structure_pipeline

FAIL: testDoubleBondStereoProblem1 (test.test_standardizer.TestCase)
a problem found in testing
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/ChEMBL_Structure_Pipeline/chembl_structure_pipeline/test/test_standardizer.py", line 1655, in testDoubleBondStereoProblem1
    self.assertNotEqual(omolb.find('13 12  1  6'), -1)
AssertionError: -1 == -1

I'll raise an issue

[eloyfelix]

Hi Dan, many thanks for opening the issue and the pull request.

There are 3 issues in here:

Adding rdkit-pypi as an extras_require: That's a good idea but what it doesn't look that nice is the need of changing the version in 2 files instad of one. We were using option 6 from here which was simple and worked for distributing the package with conda but it doesn't work with the rdkit-pypi package. We could switch to option 1 adding the setup.cfg file with the following code

[metadata]
version = attr: chembl_structure_pipeline.__version__

Tests: You can run them within the project directory running python -m unittest discover or nosetests --with-doctest like we do in the CI or running python -m unittest discover chembl_structure_pipeline if you're ouside the project directory. Relative paths should be fine.

issue https://github.com/chembl/ChEMBL_Structure_Pipeline/issues/39. Which I've just confirmed and it will need some work.

[djm-healx]

Many thanks for your prompt reply @eloyfelix - much appreciated. No problem - happy to help.

I've added a Makefile for the test command, in case this is useful in the future.

After implementing your suggestion of setup.cfg, I thought this could potentially be taken one step further by adding bump2version for automatic version increments (so it could be that make increment-minor is used after changes are made in the future). More than happy to roll back this part though if preferred, as it is perhaps unnecessary.

[eloyfelix]

I'm closing because I just merged: https://github.com/chembl/ChEMBL_Structure_Pipeline/pull/42 but many thanks for reporting the issues and thank you for the patience. I'll soon make a build of the package so it can be pip installed.